Re: [gmx-users] area per lipid

2012-12-08 Thread Peter C. Lai
Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are restrained runs to remove/dampen clashes and prevent crashes but if you are already running a full md simulation then you don't need to redo those steps. Also, I don't use DispCorr for C36 lipids (some debates about that can b

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-08 Thread James Starlight
Today I've performed test simulation of the protein-cAMP complex with the charmm27 force field and obtain good stable system. I've compared polar contacts of my complex ( ligand have been done with SwissParam) with the X-ray structure of that protein solved with the same complex and obtained simila

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-08 Thread Peter C. Lai
On 2012-12-08 03:20:54AM -0800, James Starlight wrote: > 1- on what assumptions that blocks were generated ? This appears to be a swissparm-specific question. I don't know what algorithms it uses to match what are essentially pharmacophores in the new molecule with the common individual blocks it

[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us

2012-12-08 Thread benjfitz
This is fixed in 4.6-beta1, though I am using the mpi version instead of the single-node threaded version. -- View this message in context: http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5003594.html Sent from the GROMACS Users Forum m

[gmx-users] Scientific notation in .itp files

2012-12-08 Thread Andrew DeYoung
Hi, I have been trying to rigorously check my .itp (topology) files for errors. Is it true that .itp files allow scientific notation? For example, suppose that I want to specify sigma = 0.35 nm in ffnonbonded.itp. If I enter either 3.5e-1 or 3.5E-1 will these entries indeed specify

Re: [gmx-users] Scientific notation in .itp files

2012-12-08 Thread Justin Lemkul
On 12/8/12 12:53 PM, Andrew DeYoung wrote: Hi, I have been trying to rigorously check my .itp (topology) files for errors. Is it true that .itp files allow scientific notation? For example, suppose that I want to specify sigma = 0.35 nm in ffnonbonded.itp. If I enter either 3.5e-1 or

[gmx-users] What is the purpose of the [ pairs ] section?

2012-12-08 Thread Andrew DeYoung
Hi, I am sure that this is a rather basic question, but I am wondering if you can please help me to understand something described in the manual. What is the purpose of the [ pairs ] section of an .itp file? What information does it contain? Section 5.3.4 (page 112) of the version 4.5.4 manua